Generally you'd probably use a PVC LB on the exterior of the home to change directions with, and a junction box on the inside of the home... Unfortunately I'd rather not have an access panel in a finished bathroom to keep the junction box legal.

So instead I'd like to use a larger PVC weather tight junction box on the exterior of the home, rather than a smaller LB, that way I can splice my THWN to my NMD90 in that box rather than inside the home.

I'm just not sure what the proper way of running 12/2 NMD90 through the exterior wall into the PVC box is... I assume I should use a PVC nipple, but what about the interior end of the nipple, do I just need a bushing of some sort?

You are over the border and I think under a little different rule than us southerners.
Down here we don’t like the idea of having NM cable outside even for a short distance. I would recommend that you use a UF cable to the junction box and don’t see anything wrong with the installation other than the cable going through the wall to be made up outside.

I'm just not sure what the proper way of running 12/2 NMD90 through the exterior wall into the PVC box is... I assume I should use a PVC nipple, but what about the interior end of the nipple, do I just need a bushing of some sort?

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Female connector or a male (with a bushing if larger than 1/2") should be fine.

You are over the border and I think under a little different rule than us southerners.
Down here we don’t like the idea of having NM cable outside even for a short distance. I would recommend that you use a UF cable to the junction box and don’t see anything wrong with the installation other than the cable going through the wall to be made up outside.

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The cable itself wouldn't ever be outside, it would come into the backside of the weather-tight junction box on the exterior.

Whoever installed this junction box, simply drilled a hole in the back of the box... I'd rather have a pvc connector that would at least reach through the sheathing... Or am I creating more work for myself?

Except for the lack of a connector into the back of that box this is a commonly accepted trade practice.

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That connector is what I wanted to clarify... I suppose almost any type of connector would "work", but I'd like to know what the best practice is whenever I do something. Is there no requirement for the connector to clamp the cable where it enters the box?